Additional File 8. Additional loci associated with important agronomic traits identified using genome-wide association analyses
Trait / Chr.A / MSSB P value / Total SNPsC / Region gg / Average diff.D / Data setE / Novel lociF / Known genes/QTLG / Ref.HStart / End
100 seed weight / 4 / 2.71E-07 / 4 / 21429333 / 33248973 / 1.7 / G / 45-3 / SoyBase
9 / 5.47E-07 / 2 / 47291620 / 47291622 / 1.4 / G / *
Yield / 9 / 2.97E-07 / 1 / 21579839 / 21579839 / 445 / S / 13-1 / SoyBase
10 / 4.26E-07 / 1 / 51501283 / 51501283 / 466 / S / *
16 / 1.38E-08 / 5 / 32507199 / 36750444 / 694 / S / 23-3; 21-5 / SoyBase
19 / 1.30E-07 / 2 / 34015909 / 34038285 / 740 / S / *
AChr., chromosome number
BMSS, most significant SNP based on Bonferroni correction P<0.01
BTotal SNPs and regions including SNPs in 100% linkage disequilibrium with significant SNPs at Bonferroni correction P<0.01
DAverage difference in number of days to maturity, flowering, pod filling, 100 seed weight (mg) or yield (kg ha-1) between the different haplotypes of the most significant SNP (MSS) within the locus
EData set(s) in which the significant locus was detected. M, merged data set; G, genotyping-by-sequencing data set; M, SoySNP50K microarray data set.
FLoci not reported in SoyBase.org or recent literature for seed weight or seed yield. Loci lacking stars represent known or previously reported loci, some of which genes are known and identified in the “Known Genes” column. Not all known loci have had associated genes identified.
GLoci with known and identified genes or QTL previously reported as associated with the trait of interest.
HReferences referring to genes or QTL previously identified. SoyBase refers to QTLs reported in the SoyBase database (